miR-21-3p TargetsElovl5and Regulates Triglyceride Production in Mammary Epithelial Cells of Cow

Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture-Based Systems

Body conformation traits assessed based on visual scores are widely used in Zebu cattle breeding programs. The aim of this study was to identify genomic regions and biological pathways associated with body conformation (CONF), finishing precocity (PREC), and muscling (MUSC) in Nellore cattle. The measurements based on visual scores were collected in 20,807 animals raised in pasture-based systems in Brazil. In addition, 2775 animals were genotyped using a 35 K SNP chip, which contained 31,737 single nucleotide polymorphisms after quality control. Single-step GWAS was performed using the BLUPF90 software while candidate genes were identified based on the Ensembl Genes 69. PANTHER and REVIGO platforms were used to identify key biological pathways and STRING to create gene networks. Novel candidate genes were revealed associated with CONF, including ALDH9A1, RXRG, RAB2A, and CYP7A1, involved in lipid metabolism. The genes associated with PREC were ELOVL5, PID1, DNER, TRIP12, and PLCB4, which are related to the synthesis of long-chain fatty acids, lipid metabolism, and muscle differentiation. For MUSC, the most important genes associated with muscle development were SEMA6A, TIAM2, UNC5A, and UIMC1. The polymorphisms identified in this study can be incorporated in commercial genotyping panels to improve the accuracy of genomic evaluations for visual scores in beef cattle.

Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig

Pigs' backfat quality has an important impact on the quality of pork and pork products and has a strong relationship with nutrition and sensory characteristics. This study aimed to identify the related candidate genes of backfat quality and to preliminary clarify the molecular regulatory mechanism underlying pig backfat quality phenotypes. Expression assessments of long non-coding RNA (lncRNA) and mRNA profiling in backfat from high-quality (firm and white) and low-quality (soft and yellow) Beijing Black pigs were performed by RNA sequencing. Significantly different expressions were observed in 610 protein-coding genes and 290 lncRNAs between the two groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation showed that some candidate differentially expressed genes that participate in lipid-related pathways and pigmentation terms may play a role in backfat quality in pigs. The cis-target and trans-target genes were predicted to explore the regulatory function of lncRNAs, and integrative analyses of different expression lncRNAs targets and different expression genes were performed. The results showed the regulatory networks of lncRNA-mRNA related to backfat quality, and our study obtained strong candidate genes for backfat quality: ELOVL5, SCD, DGAT2, SLC24A5, and TYRP1, which were involved in fat metabolism, adipogenesis regulation, and pigmentation. To our knowledge, this study is the first to demonstrate the molecular genetic mechanisms of backfat quality in pigs, and these findings improve the current understanding of backfat quality mechanisms and provide a foundation for further studies.

Bta-miR-33a affects gene expression and lipid levels in Chinese Holstein mammary epithelial cells

MicroRNAs (miRNAs) are non-coding single-stranded RNA molecules of about 19-25 nucleotides in length that regulate different biological processes, including lipid metabolism. In this study, we explored the effect of bta-miR-33a on lipid metabolism in bovine mammary epithelial cells (BMECs) of Chinese Holstein for the first time. For this purpose, the plasmids of bta-miR-33a mimic, bta-miR-33a inhibitor and bta-miR-33a negative control were constructed to overexpress or repress bta-miR-33a in BMECs. The effects of plasmid transfection were analysed by examining the mRNA and protein expression levels of ELOVL6 and the intracellular triglycerides. The results showed that bta-miR-33a directly inhibited the expression of ELOVL6 in BMECs; decreased the mRNA levels of ELOVL5, HACD2, CPT1A and MSMO1; and increased the mRNA level of ALOX15. Sequence bta-miR-33a also increased the contents of triglycerides in the cells, presumably as a consequence of these gene expression changes. In summary, the results of the present study suggest that bta-miR-33a regulates lipid metabolism by targeting ELOVL6, which might be a potential molecular marker of milk fat composition.

Deciphering the Key Regulatory Roles of KLF6 and Bta-miR-148a on Milk Fat Metabolism in Bovine Mammary Epithelial Cells

MicroRNAs (miRNAs) are non-coding RNAs that regulate the expression of their target genes involved in many cellular functions at the post-transcriptional level. Previously, bta-miR-148a showed significantly high expression in bovine mammary epithelial cells (BMECs) of Chinese Holstein cows producing high milk fat compared to those with low milk fat content. Here, we investigated the role of bta-miR-148a through targeting Krüppel-like factor 6 (KLF6) and further analyzed the role of KLF6 in regulating fat metabolism through targeting PPARA, AMPK/mTOR/PPARG, and other fat marker genes in BMECs of Chinese Holstein. The bioinformatics analysis showed that the 3’ UTR of KLF6 mRNA possesses the binding sites for bta-miR-148a, which was further verified through dual-luciferase reporter assay. The BMECs were transfected with bta-miR-148a-mimic, inhibitor, and shNC, and the expression of KLF6 was found to be negatively regulated by bta-miR-148a. Moreover, the contents of triglyceride (TG), and cholesterol (CHO) in BMECs transfected with bta-miR-148a-mimic were significantly lower than the contents in BMECs transfected with bta-miR-148a-shNC. Meanwhile, the TG and CHO contents were significantly increased in BMECs transfected with bta-miR-148a-inhibitor than in BMECs transfected with bta-miR-148a-shNC. In addition, the TG and CHO contents were significantly decreased in BMECs upon the down-regulation of KLF6 through transfection with pb7sk-KLF6-siRNA1 compared to the control group. Contrarily, when KLF6 was overexpressed in BMECs through transfection with pBI-CMV3-KLF6, the TG and CHO contents were significantly increased compared to the control group. Whereas, the qPCR and Western blot evaluation of PPARA, AMPK/mTOR/PPARG, and other fat marker genes revealed that all of the genes were considerably down-regulated in the KLF6-KO-BMECs compared to the normal BMECs. Taking advantage of deploying new molecular markers and regulators for increasing the production of better-quality milk with tailored fat contents would be the hallmark in dairy sector. Hence, bta-miR-148a and KLF6 are potential candidates for increased milk synthesis and the production of valuable milk components in dairy cattle through marker-assisted selection in molecular breeding. Furthermore, this study hints at the extrapolation of a myriad of functions of other KLF family members in milk fat synthesis.

Identification of critical lncRNAs for milk fat metabolism in dairy cows using WGCNA and the construction of a ceRNAs network

As key regulators, long non-coding RNAs (lncRNAs) play a crucial role in the ruminant mammary gland. However, the function of lncRNAs in milk fat synthesis from dairy cows is largely unknown. In this study, we used the weighted gene co-expression network analysis (WGCNA) to comprehensive analyze the expression profile data of lncRNAs from the group's previous Illumina PE150 sequencing results based on bovine mammary epithelial cells from high- and low-milk-fat-percentage (MFP) cows, and identify core_lncRNAs significantly associated with MFP by module membership (MM) and gene significance (GS). Functional enrichment analysis (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes) of core_lncRNA target genes (co-localization and co-expression) was performed to screen potential lncRNAs regulating milk fat metabolism and further construct an interactive regulatory network of lipid metabolism-related competing endogenous RNAs (ceRNAs). A total of 4876 lncRNAs were used to construct the WGCNA. The MEdarkturquoise module among the 19 modules obtained was significantly associated with MFP (r = 0.78, p-value <0.05) and contained 64 core_lncRNAs (MM > 0.8, GS > 0.4). Twenty-four lipid metabolism-related lncRNAs were identified by core_lncRNA target gene enrichment analysis. TCONS_00054233, TCONS_00152292, TCONS_00048619, TCONS_00033839, TCONS_00153791 and TCONS_00074642 were key candidate lncRNAs for regulating milk fat synthesis. The 22 ceRNAs most likely to be involved in milk fat metabolism were constructed by interaction network analysis, and TCONS_00133813 and bta-miR-2454-5p were located at the network's core. TCONS_00133813_bta-miR-2454-5p_TNFAIP3, TCONS_00133813_bta-miR-2454-5p_ARRB1 and TCONS_00133813_bta-miR-2454-5p_PIK3R1 are key candidate ceRNAs associated with milk fat metabolism. This study provides a framework for the co-expression module of MFP-related lncRNAs in ruminants, identifies several major lncRNAs and ceRNAs that influence milk fat synthesis, and provides a new understanding of the complex biology of milk fat synthesis in dairy cows.

RNA-Seq Reveals the Role of miR-29c in Regulating Inflammation and Oxidative Stress of Bovine Mammary Epithelial Cells

Healthy mammary gland is essential for milk performance in dairy cows. MicroRNAs (miRNAs) are the key molecules to regulate the steady state of mammary gland in dairy cows. This study investigated the potential role of miR-29c in bovine mammary epithelial cells (bMECs). RNA sequencing (RNA-seq) was used to measure the transcriptome profile of bovine mammary epithelial cells line (MAC-T) transfected with miR-29c inhibitor or negative control (NC) inhibitor, and then differentially expressed genes (DEGs) were screened. The results showed that a total of 42 up-regulated and 27 down-regulated genes were found in the miR-29c inhibitor group compared with the NC inhibitor group. The functional enrichment of the above DEGs indicates that miR-29c is a potential regulator of oxidative stress and inflammatory response in bMECs through multiple genes, such as forkhead box O1 (FOXO1), tumor necrosis factor-alpha (TNF-α), and major histocompatibility complex, class II, DQ alpha 5 (BoLA-DQA5) in the various biological process and signaling pathways of stress-activated mitogen-activated protein kinase (MAPK) cascade, Epstein-Barr virus infection, inflammatory bowel disease, etc. The results imply that miR-29c plays an important role in a steady state of bMECs or cow mammary gland and may be a potential therapeutic target for mastitis in dairy cows.

Ovine ELOVL5 and FASN genes polymorphisms and their correlations with sheep tail fat deposition

Reducing tail fat deposition can increase the economic value of a carcass and improve feed efficiency. This study aimed to explore ELOVL5 and FASN polymorphisms associated with tail fat deposition and their expression levels of sheep. Association analysis showed that ELOVL5 synonymous mutation g.62534 C > T was associated with tail width, tail fat weight, and relative tail fat weight (P < 0.05). FASN synonymous mutation g.12694 A > G was associated with tail length and width (P < 0.05). Combined effect analyses indicated significant differences between the combined genotypes and tail fat deposition. Quantitative real-time reverse transcription PCR indicated that the ELOVL5 and FASN expression levels were significantly higher in tail fat than in other tissues (P < 0.05). ELOVL5 expression levels in tail-fat tissue of big-tail sheep was significantly higher than that in small-tail sheep (P < 0.01). FASN expression levels were significantly higher in tail-fat tissue of small-tail sheep than in that of big-tail sheep (P < 0.05). During development, ELOVL5 tail fat expression increased significantly from 0 to 6 months old (P < 0.05), and FASN expression at 3 months old was significantly higher than that at 0 (minimum) and 6 months old (P < 0.05). Therefore, ELOVL5 and FASN polymorphisms could represent new candidate molecular markers and targets to reduce tail fat deposition in sheep.

Progress on the Regulation of Ruminant Milk Fat by Noncoding RNAs and ceRNAs

Milk fat is not only a key factor affecting the quality of fresh milk but also a major target trait forbreeding. The regulation of milk fat involves multiple genes, network regulation and signal transduction. To explore recent discoveries of pathway regulation, we reviewed the published literature with a focus on functional noncoding RNAs and epigenetic regulation in ruminants. Results indicate that miRNAs play key roles in the regulation of milk fat synthesis and catabolism in ruminants. Although few data are available, merging evidence indicates that lncRNAs and circRNAs act on milk fat related genes through indirect action with microRNAs or RNAs in the ceRNA network to elicit positive effects on transcription. Although precise regulatory mechanisms remain unclear, most studies have focused on the regulation of the function of target genes through functional noncoding RNAs. Data to help identify factors that can regulate their own expression and function or to determine whether self-regulation involves positive and/or negative feedback are needed. Despite the growing body of research on the role of functional noncoding RNA in the control of ruminant milk fat, most data are still not translatable for field applications. Overall, the understanding of mechanisms whereby miRNA, lncRNA, circRNA, and ceRNA regulate ruminant milk fat remains an exciting area of research.

Integrative analysis of miRNAs and mRNAs revealed regulation of lipid metabolism in dairy cattle

Lipid metabolism in bovine mammary epithelial cells has been the primary focus of the research of milk fat percentage of dairy cattle. Functional microRNAs can affect lipid metabolism by regulating the expression of candidate genes. The purpose of the study was to screen and identify differentially expressed miRNAs, candidate genes, and co-regulatory pathways related to the metabolism of milk fat. To achieve this aim, we used miRNA and transcriptome data from the mammary epithelial cells of dairy cattle with high (H, 4.85%) and low milk fat percentages (L, 3.41%) during mid-lactation. One hundred ninety differentially expressed genes and 33 differentially expressed miRNAs were significantly enriched in related regulatory networks, of which 27 candidate genes regulated by 18 differentially expressed miRNAs significantly enriched in pathways related to lipid metabolism (p < 0.05). Target relationships between PDE4D and bta-miR-148a, PEG10 and bta-miR-877, SOD3 and bta-miR-2382-5p, and ADAMTS1 and bta-miR-2425-5p were verified using luciferase reporter assays and quantitative RT-PCR. The detection of triglyceride production in BMECs showed that bta-miR-21-3p and bta-miR-148a promote triglyceride synthesis, whereas bta-miR-124a, bta-miR-877, bta-miR-2382-5p, and bta-miR-2425-5p inhibit triglyceride synthesis. The conjoint analysis could identify functional miRNAs and regulatory candidate genes involved in lipid metabolism within the co-expression networks of the dairy cattle mammary system, which contributes to the understanding of potential regulatory mechanisms of genetic element and gene signaling networks involved in milk fat metabolism.

MiR-485 targets the DTX4 gene to regulate milk fat synthesis in bovine mammary epithelial cells

MicroRNAs (miRNAs) are mRNA suppressors that regulate a variety of cellular and physiological processes, including cell proliferation, apoptosis, triglyceride synthesis, fat formation, and lipolysis, by post-transcriptional processing. In previous studies, we isolated and sequenced miRNAs from mammary epithelial cells from Chinese Holstein cows with high and low milk fat percentages. MiR-485 was one of the significantly differentially expressed miRNAs that were identified. In the present study, the relationship between the candidate target gene DTX4 and miR-485 was validated by bioinformatics and real-time fluorescent quantitative PCR (qRT-PCR) and Western blot (WB) analyses in bovine mammary epithelial cells (bMECs). The results indicated that miR-485 negatively regulated the mRNA expression of the target gene DTX4. Furthermore, an shRNA interference vector for the target gene DTX4 was constructed successfully, and it increased the triglyceride content and reduced the cholesterol content of transfected cells. These results suggest that miR-485 may affect the contents of triglycerides (TGs) and cholesterol (CHOL) by targeting the DTX4 gene. This study indicates that miR-485 has a role in regulating milk fat synthesis and that miR-485 targets the DTX4 gene to regulate lipid metabolism in bMECs. These findings contribute to the understanding of the functional significance of miR-485 in milk fat synthesis.

Lipopolysaccharide inhibits triglyceride synthesis in dairy cow mammary epithelial cells by upregulating miR-27a-3p, which targets the PPARG gene

The fat content of milk determines the quality of milk, and triglycerides are the major components of milk fat. Milk fat synthesis is regulated by many factors. Lipopolysaccharide (LPS) has been shown to inhibit milk fat synthesis in bovine mammary epithelial cells, but research on the underlying mechanisms has been limited. MicroRNA (miRNA) are involved in many physiological processes, but there have been few studies on their regulation in milk fat synthesis. In this study, we aimed to investigate whether LPS upregulates miR-27a-3p, which targets PPARG, thereby inhibiting the synthesis of triglycerides in a dairy cow mammary epithelial cell line (MAC-T). After LPS stimulation of MAC-T cells, PPARG gene expression and milk fat synthesis were inhibited. TargetScan software was used to predict miRNA targeting PPARG, and miR-27a-3p was selected as a candidate. A dual luciferase reporter assay further confirmed the targeting connection between miR-27a-3p and the PPARG gene. To investigate the functions of miR-27a-3p, miR-27a-3p mimic and inhibitors were transfected into MAC-T cells. The mRNA and protein levels of PPAR-γ were negatively correlated with the expression of miR-27a-3p. Lipid droplet accumulation and triglyceride synthesis were also negatively correlated with miR-27a-3p expression. Inhibition of miR-27a-3p partially reversed the LPS-induced decreases in PPARG expression and milk fat synthesis. In summary, our results reveal that LPS can inhibit MAC-T cell milk fat synthesis by upregulating miR-27a-3p, which targets the PPARG gene.

miR-2382-5p Regulates Lipid Metabolism by Targeting NDRG2 in Mammary Epithelial Cells of Dairy Cattle

microRNA is a class of single-stranded RNA molecules of about 22-24 nucleotides in length, which regulate a variety of biological processes, including lipid metabolism and triglyceride synthesis at transcriptional and translational levels by degrading target mRNAs or interfering with the protein production. In this study, the effect of miR-2382-5p on triglyceride levels was examined in bovine mammary epithelial cells (BMECs), and the results showed that miR-2382-5p could decrease the content of triglyceride. Furthermore, miR-2382-5p regulated the expression of lipoprotein lipase (LPL), peroxisome proliferator-activated receptor gamma co-activator 1beta (PPARGC1B), hormone-sensitive lipase (HSL), and peroxisome proliferator-activated receptor gamma (PPARγ), which are known to increase triglyceride decomposition in lipid metabolism. Luciferase reporter assay and quantitative real-time PCR (qPCR) validated that miR-2382-5p downregulated the mRNA expression of target gene N-myc downstream-regulated gene 2 (NDRG2) by specifically recognizing and binding to its 3'-untranslated region (UTR). Meanwhile, overexpression of NDRG2 led to increased triglyceride and cholesterol production in BMECs. In summary, this study suggested that miR-2382-5p regulated lipid metabolism by targeting NDRG2, which might be a potential target for molecular manipulation of milk fat composition to produce healthy milk. This study also provided basic data for further understanding lipid metabolism in dairy cattle.